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#+ Wrnap::Rna::Box
#<=> Wrnap::Package::EnergyGrid2d::Row2d
#== Wrnap::Rna
#RNA Top Level Namespace
#__data__ Wrnap::Rna::Metadata::Container
#__rna__ Wrnap::Rna::Metadata::Container
#_id Wrnap::Rna::Context
#accession Wrnap::Rna::Context
#add_node Wrnap::Rna::TreePlanter
aligned_distributions Wrnap::Package::EnergyGrid2d
#apply! Wrnap::Rna::Helix
balanced_consensus_from_sequence Wrnap::Etl::Stockholm
#barrier Wrnap::Package::TabuPath::Path
#barrier Wrnap::Package::Kinwalker::Node
#base_flags Wrnap::Global::Runner::InstanceMethods
#base_pairs Wrnap::Rna::Extensions::OneStructureBasedMethods
#best_weight Wrnap::Package::TabuPath::Path
#between Wrnap::Rna::Constraints::ConstraintBox
#bin Wrnap::Package::Subopt
#boltzmann_probability Wrnap::Rna::Extensions::InstanceMethods
bootstrap Wrnap::Package::Base
#bp_distance Wrnap::Rna::Extensions::TwoStructureBasedMethods
#build_constraints Wrnap::Rna::Constraints::InstanceMethods
#build_tree Wrnap::Rna::TreePlanter
#chain Wrnap::Global::Chainer::InstanceMethods
#coalesce Wrnap::Rna::TreePlanter
#coalesce! Wrnap::Rna::TreePlanter
#collapsed_helices Wrnap::Rna::Extensions::OneStructureBasedMethods
#comment Wrnap::Rna
consensus_structure_from_file Wrnap::Etl::Stockholm
const_missing Wrnap::Package
#constraint_mask Wrnap::Rna::Constraints::InstanceMethods
#constraints Wrnap::Rna::Constraints::ConstraintBox
convert_infernal_to_dot_bracket Wrnap::Etl::Infernal
#coord_options Wrnap::Rna::Context
#coord_window Wrnap::Rna::Context
#copy_name_from Wrnap::Rna
#counts Wrnap::Package::Rnabor
#data Wrnap::Package::Base
debug Wrnap
debug= Wrnap
#debugger Wrnap::Package::Base
debugger Wrnap
#depth_signature Wrnap::Rna::TreePlanter
#deserialize Wrnap::Global::Yaml
#detached_copy Wrnap::Rna::TreeStem
#dishuffle Wrnap::Rna::Extensions::InstanceMethods
#distribution Wrnap::Package::Fftbor
#distribution Wrnap::Package::Fftbor2d
#distribution Wrnap::Package::Rnabor
#distribution Wrnap::Package::Rna2dfold
#distribution Wrnap::Package::EnergyGrid2d::EnergyGrid2dWrapper
dot_bracket_from_stockholm Wrnap::Etl::Stockholm
#down_coord Wrnap::Rna::Context
#each Wrnap::Rna::Box
#each Wrnap::Package::EnergyGrid2d
#each Wrnap::Package::FftPopulation::PopulationProportion
#eigenvalues Wrnap::Package::Spectral
#empty_structure Wrnap::Rna
#end_to Wrnap::Rna::Constraints::ConstraintBox
#energy Wrnap::Package::Kinwalker::Node
#energy_barrier Wrnap::Package::Kinwalker::Node
#ensemble Wrnap::Package::EnergyGrid2d::Row2d
#ensemble_energy Wrnap::Package::FoldConstrained
#ensemble_energy Wrnap::Package::Fold
#eql? Wrnap::Rna
#equilibrium Wrnap::Package::FftEq
#exec_exists? Wrnap::Global::Runner::ClassMethods
#exec_name Wrnap::Global::Runner::ClassMethods
#exec_name Wrnap::Global::Runner::InstanceMethods
#expected_k Wrnap::Package::Xbor
#extend! Wrnap::Rna::Context
#extend_interior_loops! Wrnap::Rna::TreePlanter
#extend_tree Wrnap::Rna::TreePlanter
#extend_tree! Wrnap::Rna::TreePlanter
fit_structure_to_sequence Wrnap::Etl::Stockholm
#flags Wrnap::Package::Base
#formatted_string Wrnap::Rna
#freeze Wrnap::Rna::Constraints::ConstraintBox
#from Wrnap::Rna::Context
#from Wrnap::Rna::Constraints::ConstraintData
#full_distribution Wrnap::Package::Xbor
#full_path? Wrnap::Package::TabuPath::Path
#fuse Wrnap::Rna::TreePlanter
#fuse! Wrnap::Rna::TreePlanter
#gc_content Wrnap::Rna::Extensions::InstanceMethods
#generate_sequence Wrnap::Rna::Extensions::ClassMethods
#get_pairings Wrnap::Rna::Extensions::OneStructureBasedMethods
#global_structural_shuffle Wrnap::Rna::Extensions::InstanceMethods
graph Wrnap::Graphing::R
#hamming_distance Wrnap::Rna::Extensions::InstanceMethods
#handle_interior_loops! Wrnap::Rna::TreePlanter
#helices Wrnap::Rna::Extensions::OneStructureBasedMethods
histogram Wrnap::Graphing::R
#i Wrnap::Package::EnergyGrid2d::Row2d
#i Wrnap::Rna::Loop
#i Wrnap::Rna::Helix
#identifier Wrnap::Rna::Context
#in Wrnap::Rna::Loop
#in Wrnap::Rna::Helix
included Wrnap::Global::Runner
included Wrnap::Rna::Constraints
included Wrnap::Rna::Metadata
included Wrnap::Rna::Extensions
included Wrnap::Rna::Metadata::InstanceMethods
included Wrnap::Global::Chainer
inherited Wrnap::Package::EnergyGrid2d
init_from_array Wrnap::Rna
init_from_context Wrnap::Rna
init_from_entrez Wrnap::Rna::Context
init_from_fasta Wrnap::Rna
init_from_hash Wrnap::Rna
init_from_self Wrnap::Rna
init_from_string Wrnap::Rna::Context
init_from_string Wrnap::Rna
#initialize Wrnap::Rna::Loop
#initialize Wrnap::Package::TabuPath::Path
#initialize Wrnap::Rna::Helix
#initialize Wrnap::Rna::Context
#initialize Wrnap::Package::EnergyGrid2d::Row2d
#initialize Wrnap::Rna::TreePlanter
#initialize Wrnap::Package::Base
#initialize Wrnap::Rna::Constraints::ConstraintData
#initialize Wrnap::Rna::Box
#initialize Wrnap::Package::Kinwalker::Node
#initialize Wrnap::Rna
#initialize Wrnap::Package::FftPopulation::PopulationProportion
#initialize Wrnap::Rna::Metadata::Container
#initialize Wrnap::Rna::Constraints::ConstraintBox
#inside Wrnap::Rna::Constraints::ConstraintBox
#inspect Wrnap::Rna::Loop
#inspect Wrnap::Package::TabuPath::Path
#inspect Wrnap::Rna::Helix
#inspect Wrnap::Rna::TreePlanter
#inspect Wrnap::Rna::Constraints::ConstraintData
#inspect Wrnap::Package::Base
#inspect Wrnap::Package::EnergyGrid2d::Row2d
#inspect Wrnap::Rna::Box
#inspect Wrnap::Rna::Metadata::Container
#inspect Wrnap::Rna::Constraints::ConstraintBox
#inspect Wrnap::Rna
#inspect Wrnap::Package::Xbor
#inspect Wrnap::Package::EnergyGrid2d
#inspect Wrnap::Package::FftPopulation::PopulationProportion
#inspect Wrnap::Rna::Context
#j Wrnap::Rna::Loop
#j Wrnap::Rna::Helix
#j Wrnap::Package::EnergyGrid2d::Row2d
#k Wrnap::Rna::Helix
#k_p_points Wrnap::Package::Xbor
#kind_of? Wrnap::Rna::Box
#l Wrnap::Rna::Helix
#length Wrnap::Rna::Loop
#length Wrnap::Rna::Helix
#length Wrnap::Rna::Constraints::ConstraintData
#length Wrnap::Package::TabuPath::Path
line_graph Wrnap::Graphing::R
load_all Wrnap::Etl::Stockholm
load_all Wrnap::Rna::Box
load_all RNA
load_all Wrnap::Etl::Infernal
#local_structural_dishuffle Wrnap::Rna::Extensions::InstanceMethods
#local_structural_shuffle Wrnap::Rna::Extensions::InstanceMethods
lookup Wrnap::Package
#loop_regions Wrnap::Rna::Extensions::OneStructureBasedMethods
#loops_and_helices Wrnap::Rna::Extensions::OneStructureBasedMethods
#mask! Wrnap::Rna::Constraints::ConstraintBox
#mask_helix! Wrnap::Rna::Constraints::ConstraintBox
#mask_loop! Wrnap::Rna::Constraints::ConstraintBox
#mask_region! Wrnap::Rna::Constraints::ConstraintBox
matrix_heatmap Wrnap::Graphing::R
#max_bp_distance Wrnap::Rna::Extensions::OneStructureBasedMethods
#merge! Wrnap::Rna::Helix
#merge_interior_loops! Wrnap::Rna::TreePlanter
#meta Wrnap::Rna::Metadata::InstanceMethods
#meta_rna Wrnap::Rna::Metadata::InstanceMethods
#metadata Wrnap::Rna
#method_missing Wrnap::Rna::Metadata::Container
#method_missing Wrnap::Rna::Constraints::ConstraintBox
#method_missing Wrnap::Rna::TreePlanter
#method_missing Wrnap::Rna::TreeStem
#method_missing Wrnap::Rna::Box
#method_missing Wrnap::Rna
method_missing RNA
#mfe Wrnap::Package::Fold
#mfe Wrnap::Package::Eval
#mfe Wrnap::Package::FoldConstrained
#mfe_rna Wrnap::Package::FoldConstrained
#mfe_rna Wrnap::Package::Fold
#mfpt Wrnap::Package::Mfpt
#mfpt Wrnap::Package::FftMfpt
#mfpt Wrnap::Package::Kinwalker
#minus_strand? Wrnap::Rna::Context
#n Wrnap::Rna::Constraints::ConstraintBox
na_sequence_from_entrez Wrnap::Global::Entrez
#name Wrnap::Rna::Constraints::ConstraintData
#name Wrnap::Rna::Loop
#name Wrnap::Rna::Helix
#no_structure Wrnap::Rna
#nodes Wrnap::Package::Kinwalker
#non_zero_shells Wrnap::Package::Rnabor
#one_structure Wrnap::Rna
overlay Wrnap::Graphing::R
#p Wrnap::Package::EnergyGrid2d::Row2d
parse Wrnap::Package::Xbor
parse_hit Wrnap::Etl::Infernal
#partition Wrnap::Package::Rnabor
#partition Wrnap::Package::Fftbor
#path Wrnap::Package::TabuPath::Path
#paths Wrnap::Package::TabuPath
#plus_strand? Wrnap::Rna::Context
#position Wrnap::Package::EnergyGrid2d::Row2d
#post_process Wrnap::Package::Spectral
#post_process Wrnap::Package::FftMfpt
#post_process Wrnap::Package::Heat
#post_process Wrnap::Package::Fold
#post_process Wrnap::Package::Eval
#post_process Wrnap::Package::Mfpt
#post_process Wrnap::Package::FoldConstrained
#post_process Wrnap::Package::FftPopulation
#post_process Wrnap::Package::TabuPath
#post_process Wrnap::Package::Kinwalker
#post_process Wrnap::Package::Subopt
#post_process Wrnap::Package::FftEq
#postorder_traversal Wrnap::Rna::TreeStem
#pp Wrnap::Rna::TreePlanter
#pp Wrnap::Rna::Box
#pp Wrnap::Rna
#pre_run_check Wrnap::Global::Runner::InstanceMethods
#preorder_traversal Wrnap::Rna::TreeStem
#proportion_over_time Wrnap::Package::FftPopulation::PopulationProportion
#proportion_points Wrnap::Package::FftPopulation::PopulationProportion
#prune! Wrnap::Rna::Constraints::ConstraintBox
prune_gaps Wrnap::Etl::Stockholm
pull_infernal_hit_sequence Wrnap::Etl::Infernal
pull_infernal_hit_structure Wrnap::Etl::Infernal
#quick_plot Wrnap::Package::Xbor
#quick_plot Wrnap::Package::EnergyGrid2d
random RNA
#rebuild_tree Wrnap::Rna::TreePlanter
#recursively_merge_flags Wrnap::Global::Runner::InstanceMethods
#reindex! Wrnap::Rna::Helix
#response Wrnap::Package::Base
#rna Wrnap::Rna::TreePlanter
#rna Wrnap::Package::TabuPath::Path
#rna Wrnap::Rna::Constraints::ConstraintBox
rna_sequence_from_entrez Wrnap::Global::Entrez
rnafold_ensemble_energy Wrnap::Global::Parser
rnafold_mfe Wrnap::Global::Parser
rnafold_mfe_structure Wrnap::Global::Parser
#rnas Wrnap::Rna::Box
roc Wrnap::Graphing::R
roc_overlay Wrnap::Graphing::R
#root Wrnap::Rna::TreePlanter
#run Wrnap::Rna
#run Wrnap::Global::Runner::InstanceMethods
#run Wrnap::Global::Runner::ClassMethods
#run_command Wrnap::Package::Xbor
#run_command Wrnap::Package::Plot
#run_command Wrnap::Package::FftEqBase
#run_command Wrnap::Package::Mfpt
#run_command Wrnap::Package::FftMfpt
#run_command Wrnap::Package::Rna2dfold
#run_command Wrnap::Package::TabuPath
#run_command Wrnap::Package::Varna
#run_command Wrnap::Global::Runner::InstanceMethods
#run_command Wrnap::Package::Spectral
#run_command Wrnap::Package::Fftbor2d
#run_in_parallel Wrnap::Rna::Box
#runtime Wrnap::Package::Base
scatterplot Wrnap::Graphing::R
#second_structure Wrnap::Rna
#seq_from Wrnap::Rna::Context
#seq_to Wrnap::Rna::Context
#sequence Wrnap::Rna::Context
#sequence Wrnap::Rna
sequence_from_entrez Wrnap::Global::Entrez
#serialize Wrnap::Global::Yaml
set_of_points Wrnap::Package::EnergyGrid2d
#show_constraints Wrnap::Rna::Constraints::InstanceMethods
#shuffle Wrnap::Rna::Extensions::ClassMethods
simple_rna_sequence Wrnap::Global::Entrez
#specific_heats Wrnap::Package::Heat
#start_to Wrnap::Rna::Constraints::ConstraintBox
#starting_population Wrnap::Package::FftPopulation
#strand Wrnap::Rna::Context
#stringify_flags Wrnap::Global::Runner::InstanceMethods
#structure Wrnap::Package::Kinwalker::Node
#structure Wrnap::Package::Fold
#structure Wrnap::Package::FoldConstrained
#structure Wrnap::Rna
#structure_from_bp_list Wrnap::Rna::Extensions::ClassMethods
#structures Wrnap::Package::Subopt
#symbol Wrnap::Rna::Constraints::ConstraintData
#target_population Wrnap::Package::FftPopulation
#temp_fa_file! Wrnap::Rna
theta_filter Wrnap::Etl::Stockholm
#time Wrnap::Package::Kinwalker::Node
#time_kinetics Wrnap::Package::Spectral
#time_points Wrnap::Package::FftPopulation::PopulationProportion
#time_range Wrnap::Package::FftPopulation::PopulationProportion
#to Wrnap::Rna::Constraints::ConstraintData
#to Wrnap::Rna::Context
#to_csv Wrnap::Package::EnergyGrid2d::Row2d
#to_csv Wrnap::Package::Xbor
#to_csv Wrnap::Package::EnergyGrid2d
#to_csv! Wrnap::Package::Xbor
#to_csv! Wrnap::Package::EnergyGrid2d
#to_loops Wrnap::Rna::Helix
#to_s Wrnap::Rna::Constraints::ConstraintBox
#total_count Wrnap::Package::Rnabor
#total_count Wrnap::Package::Fftbor
#transcribed Wrnap::Package::Kinwalker::Node
#transform_for_chaining Wrnap::Package::Mfpt
#trunk Wrnap::Rna::TreeFunctions
#two_structures Wrnap::Rna
#unpaired_regions Wrnap::Rna::TreeStem
#up_coord Wrnap::Rna::Context
#validate_coord_options Wrnap::Rna::Context
#with_tree Wrnap::Rna::TreeFunctions
#write_fa! Wrnap::Rna::Box
#write_fa! Wrnap::Rna
#wrnap Wrnap::Rna::Wrnapper